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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ), 'gf_id' => 'HOM05D001370', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001370' ), 'data_identifier' => 'HOM05D001370', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001370', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31460' => 'bna', 'A04p04680' => 'bna', 'A05p41890' => 'bna', 'A07p08790' => 'bna', 'Aa31LG10G9780' => 'aar', 'Aa31LG5G16630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4935' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2791' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1006' => 'aag', 'Actinidia00089' => 'ach', 'Actinidia01361' => 'ach', 'Actinidia01362' => 'ach', 'Actinidia02979' => 'ach', 'Actinidia08124' => 'ach', 'Actinidia08125' => 'ach', 'Actinidia26736' => 'ach', 'Actinidia29449' => 'ach', 'Actinidia34346' => 'ach', 'Actinidia37447' => 'ach', 'Ah.03g133400' => 'amhyb', 'Ah.16g107530' => 'amhyb', 'Ah.16g107540' => 'amhyb', 'AL3G16960' => 'aly', 'AL3G38290' => 'aly', 'AL5G36410' => 'aly', 'Aqoxy2G03275' => 'aox', 'Aqoxy3G01259' => 'aox', 'Aqoxy4G03041' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0H136B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.51BPXJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KM540I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8BGWM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN6D8B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V2UXPA' => 'arhy', 'AT3G06110' => 'ath', 'AT3G23610' => 'ath', 'ATR0122G003' => 'atr', 'ATR0626G123' => 'atr', 'ATR0665G352' => 'atr', 'Atru.chr11.2165' => 'acertr', 'Atru.chr12.560' => 'acertr', 'Atru.chr4.2564' => 'acertr', 'AUR62005506' => 'cqu', 'AUR62022523' => 'cqu', 'AUR62024235' => 'cqu', 'AUR62030097' => 'cqu', 'AUR62035948' => 'cqu', 'AUR62038211' => 'cqu', 'BcaB02g08434' => 'bca', 'BcaB04g20437' => 'bca', 'BcaB06g26516' => 'bca', 'BcaC02g09740' => 'bca', 'BcaC05g30055' => 'bca', 'BcaC05g30056' => 'bca', 'BcaC06g35545' => 'bca', 'BolC1t03965H' => 'bol', 'BolC4t25280H' => 'bol', 'BolC5t34773H' => 'bol', 'BolC7t41859H' => 'bol', 'BraA01t03272Z' => 'bra', 'BraA04t16180Z' => 'bra', 'BraA05t22908Z' => 'bra', 'BraA07t28670Z' => 'bra', 'C01p40090' => 'bna', 'C04p37060' => 'bna', 'C05p61140' => 'bna', 'C07p13640' => 'bna', 'CAN.G1339.10' => 'can', 'CAN.G1339.11' => 'can', 'CAN.G1339.12' => 'can', 'CAN.G1339.13' => 'can', 'CAN.G1339.14' => 'can', 'CAN.G1339.15' => 'can', 'CAN.G1339.16' => 'can', 'CAN.G1339.17' => 'can', 'CAN.G1339.18' => 'can', 'CAN.G1339.21' => 'can', 'CAN.G1339.22' => 'can', 'CAN.G1339.23' => 'can', 'CAN.G1339.24' => 'can', 'CAN.G1339.25' => 'can', 'CAN.G1339.27' => 'can', 'CAN.G1339.28' => 'can', 'CAN.G1339.29' => 'can', 'CAN.G1339.9' => 'can', 'CAN.G1447.10' => 'can', 'CAN.G1447.11' => 'can', 'CAN.G1447.13' => 'can', 'CAN.G1447.14' => 'can', 'CAN.G1447.5' => 'can', 'CAN.G1447.6' => 'can', 'CAN.G183.17' => 'can', 'CAN.G272.7' => 'can', 'CAN.G2763.1' => 'can', 'CAN.G305.21' => 'can', 'CAN.G503.2' => 'can', 'CAN.G503.3' => 'can', 'CAN.G503.4' => 'can', 'CAN.G503.5' => 'can', 'CANSAT01G0008' => 'cansat', 'CANSAT11G2164' => 'cansat', 'CANSAT56G0616' => 'cansat', 'CARHR080620' => 'chi', 'CARHR099540' => 'chi', 'CARHR165270' => 'chi', 'Carub.0003s0555' => 'cru', 'Carub.0003s2384' => 'cru', 'Carub.0005s2193' => 'cru', 'Ca_07181_v3' => 'car', 'Ca_17784_v3' => 'car', 'Ca_21596_v3' => 'car', 'Ca_25134_v3' => 'car', 'Ca_29878_v3' => 'car', 'CBR_g53715' => 'cbr', 'CBR_g8320' => 'cbr', 'CBR_g8330' => 'cbr', 'Cc02_g08460' => 'ccan', 'Cc03_g03170' => 'ccan', 'Cc11_g15980' => 'ccan', 'CDE02G2968' => 'cde', 'CDE05G3339' => 'cde', 'CDE09G1201' => 'cde', 'Cfa001538' => 'cfa', 'Cfa009236' => 'cfa', 'Ciclev10006038m.g' => 'ccl', 'Ciclev10030706m.g' => 'ccl', 'Ciclev10031023m.g' => 'ccl', 'CiPaw.01G160500' => 'cil', 'CiPaw.01G282000' => 'cil', 'CiPaw.02G092900' => 'cil', 'CiPaw.02G180300' => 'cil', 'CiPaw.05G178100' => 'cil', 'ClCG05G025890' => 'cla', 'ClCG06G005830' => 'cla', 'ClCG07G003050' => 'cla', 'COL.COLO4_10923' => 'col', 'COL.COLO4_21656' => 'col', 'COL.COLO4_23487' => 'col', 'Cpa.g.sc16.19' => 'cpa', 'Cpa.g.sc1696.2' => 'cpa', 'Cre06.g267250' => 'cre', 'Cre08.g358554' => 'cre', 'Cre09.g395100' => 'cre', 'Cre09.g395150' => 'cre', 'Cre09.g416950' => 'cre', 'Cre17.g717300' => 'cre', 'CsaV3_5G006730' => 'csa', 'CsaV3_5G030970' => 'csa', 'CsaV3_6G018610' => 'csa', 'CSS0011197' => 'camsi', 'CSS0030500' => 'camsi', 'CSS0042782' => 'camsi', 'CSS0043177' => 'camsi', 'DCAR_002412' => 'dca', 'DCAR_007042' => 'dca', 'DCAR_015225' => 'dca', 'DCAR_019163' => 'dca', 'DCAR_026502' => 'dca', 'DCAR_030601' => 'dca', 'Dinv14740' => 'din', 'Dinv15207' => 'din', 'Dinv19360' => 'din', 'Dinv25963' => 'din', 'Dinv31410' => 'din', 'Dinv38398' => 'din', 'Duzib106G1608' => 'dzi', 'Duzib114G0713' => 'dzi', 'Duzib151G1082' => 'dzi', 'Duzib268G0753' => 'dzi', 'ECA233G1109' => 'eca', 'ECA234G0244' => 'eca', 'ECA238G4199' => 'eca', 'ECA246G1188' => 'eca', 'EL10Ac2g03456' => 'bvu', 'EL10Ac6g13878' => 'bvu', 'Eucgr.B01140' => 'egr', 'Eucgr.B01141' => 'egr', 'Eucgr.B03267' => 'egr', 'Eucgr.H03589' => 'egr', 'Eucgr.H03590' => 'egr', 'FAN03G0479' => 'fan', 'FAN06G0060' => 'fan', 'FAN06G4207' => 'fan', 'FAN07G2135' => 'fan', 'FAN07G2548' => 'fan', 'FAN10G1480' => 'fan', 'FAN12G0014' => 'fan', 'FAN12G1701' => 'fan', 'FAN12G3726' => 'fan', 'FAN17G1306' => 'fan', 'FAN17G1690' => 'fan', 'FAN17G2201' => 'fan', 'FAN22G2011' => 'fan', 'FvH4_4g14540' => 'fve', 'FvH4_4g14580' => 'fve', 'FvH4_4g14700' => 'fve', 'FvH4_4g25430' => 'fve', 'FvH4_7g21250' => 'fve', 'Glyma.02G095100' => 'gma', 'Glyma.05G174000' => 'gma', 'Glyma.07G257400' => 'gma', 'Glyma.08G131200' => 'gma', 'Glyma.11G243900' => 'gma', 'Glyma.17G016700' => 'gma', 'Glyma.18G013200' => 'gma', 'Glyma.18G286300' => 'gma', 'Gohir.A01G158600' => 'ghi', 'Gohir.A03G133000' => 'ghi', 'Gohir.A05G351500' => 'ghi', 'Gohir.A09G200100' => 'ghi', 'Gohir.A09G200300' => 'ghi', 'Gohir.A10G211900' => 'ghi', 'Gohir.D01G152100' => 'ghi', 'Gohir.D02G157300' => 'ghi', 'Gohir.D04G061200' => 'ghi', 'Gohir.D09G194400' => 'ghi', 'Gohir.D09G194500' => 'ghi', 'Gohir.D10G219900' => 'ghi', 'Gorai.002G188400' => 'gra', 'Gorai.005G176500' => 'gra', 'Gorai.006G217800' => 'gra', 'Gorai.006G217900' => 'gra', 'Gorai.011G246600' => 'gra', 'Gorai.012G068100' => 'gra', 'GSVIVG01000558001' => 'vvi', 'GSVIVG01003294001' => 'vvi', 'GSVIVG01016637001' => 'vvi', 'GSVIVG01017893001' => 'vvi', 'HanXRQChr04g0124641' => 'han', 'HanXRQChr07g0200751' => 'han', 'HanXRQChr08g0208391' => 'han', 'HanXRQChr08g0220021' => 'han', 'HanXRQChr09g0275511' => 'han', 'HanXRQChr11g0329161' => 'han', 'HanXRQChr12g0359361' => 'han', 'HanXRQChr17g0539911' => 'han', 'Haze_00957' => 'cav', 'Haze_12271' => 'cav', 'Haze_16996' => 'cav', 'Haze_26980' => 'cav', 'Hma1.2p1_0079F.1_g041160' => 'hma', 'Hma1.2p1_0207F.1_g087710' => 'hma', 'Hma1.2p1_0727F.1_g209075' => 'hma', 'Hma1.2p1_0900F.1_g234600' => 'hma', 'Hma1.2p1_1037F.1_g250560' => 'hma', 'HPP92_006595' => 'vpl', 'HPP92_006596' => 'vpl', 'HPP92_010619' => 'vpl', 'Hund22413' => 'sun', 'Hund25401' => 'sun', 'Lalb_Chr04g0257931' => 'lal', 'Lalb_Chr07g0185461' => 'lal', 'Lalb_Chr10g0091881' => 'lal', 'Lalb_Chr12g0196201' => 'lal', 'Lalb_Chr12g0204051' => 'lal', 'Lalb_Chr13g0295821' => 'lal', 'Lalb_Chr17g0336271' => 'lal', 'Lalb_Chr23g0277641' => 'lal', 'Lalb_Chr23g0277651' => 'lal', 'Lj1g0004559' => 'lja', 'Lj1P932T14' => 'lonja', 'Lj3P1060T68' => 'lonja', 'Lj4g0008975' => 'lja', 'Lj4g0018968' => 'lja', 'Lj6C575T3' => 'lonja', 'Lj6g0008047' => 'lja', 'Lsat_1_v5_gn_3_30200' => 'lsa', 'Lsat_1_v5_gn_5_76821' => 'lsa', 'Lsat_1_v5_gn_8_17260' => 'lsa', 'Manes.03G184200' => 'mes', 'Manes.07G110400' => 'mes', 'Manes.10G037800' => 'mes', 'Manes.12G020900' => 'mes', 'Manes.15G023800' => 'mes', 'Mapoly0055s0069' => 'mpo', 'Mapoly0129s0017' => 'mpo', 'MBI05_g07847_MAGBIO' => 'mbi', 'MBI19_g12617_MAGBIO' => 'mbi', 'MBI19_g41872_MAGBIO' => 'mbi', 'MBI19_g43500_MAGBIO' => 'mbi', 'MCO07G028' => 'mco', 'MCO14G426' => 'mco', 'MCO16G432' => 'mco', 'MD01G1120800' => 'mdo', 'MD07G1190200' => 'mdo', 'MD13G1103000' => 'mdo', 'MD16G1103200' => 'mdo', 'MD16G1184700' => 'mdo', 'Medtr3g086540' => 'mtr', 'Medtr4g117170' => 'mtr', 'Medtr6g071980' => 'mtr', 'Medtr7g023250' => 'mtr', 'Medtr8g089710' => 'mtr', 'MELO3C011936.2' => 'cme', 'MELO3C021405.2' => 'cme', 'MELO3C023830.2' => 'cme', 'Migut.E00215' => 'egut', 'Migut.G00292' => 'egut', 'Migut.K00621' => 'egut', 'MSTRG.10014' => 'ama', 'MSTRG.13341' => 'ama', 'MSTRG.556' => 'ama', 'MSTRG.7953' => 'ama', 'Nitab4.5_0000267g0100' => 'nta', 'Nitab4.5_0001690g0010' => 'nta', 'Nitab4.5_0001978g0050' => 'nta', 'Nitab4.5_0005184g0010' => 'nta', 'Nitab4.5_0008833g0010' => 'nta', 'Nitab4.5_0022426g0010' => 'nta', 'Nn2g10498' => 'nnu', 'Nn2g12877' => 'nnu', 'Nn3g16669' => 'nnu', 'Nn3g16719' => 'nnu', 'Oeu027194.1' => 'oeu', 'Oeu031208.1' => 'oeu', 'Oeu031877.1' => 'oeu', 'Oeu031878.1' => 'oeu', 'Oeu031879.1' => 'oeu', 'Oeu037685.1' => 'oeu', 'Oeu038639.1' => 'oeu', 'Oeu040014.3' => 'oeu', 'Oeu057549.1' => 'oeu', 'Oeu059776.1' => 'oeu', 'Oeu059777.1' => 'oeu', 'Os01g0390900' => 'osa', 'Os05g0115800' => 'osa', 'Peaxi162Scf00015g00219' => 'pax', 'Peaxi162Scf00067g00118' => 'pax', 'Peaxi162Scf00128g00446' => 'pax', 'Peaxi162Scf00196g00087' => 'pax', 'PGR004G2275' => 'pgr', 'PGR044G2712' => 'pgr', 'PGR102G1342' => 'pgr', 'PGR142G3165' => 'pgr', 'PGSC0003DMG400011726' => 'stu', 'PGSC0003DMG400023418' => 'stu', 'Phvul.001G255800' => 'pvu', 'Phvul.002G259000' => 'pvu', 'Phvul.008G015300' => 'pvu', 'Potri.008G049900' => 'ptr', 'Potri.010G033000' => 'ptr', 'Potri.010G210900' => 'ptr', 'Pp3c11_19720' => 'ppa', 'Pp3c16_10810' => 'ppa', 'Pp3c26_11530' => 'ppa', 'Pp3c7_6670' => 'ppa', 'PRCOL_00005512' => 'pco', 'PRCOL_00006891' => 'pco', 'Prupe.1G151900' => 'ppe', 'Prupe.1G242800' => 'ppe', 'Prupe.2G228100' => 'ppe', 'Psat3g184920' => 'psa', 'Psat4g031760' => 'psa', 'Psat5g091880' => 'psa', 'Psat6g069080' => 'psa', 'Psat7g059560' => 'psa', 'PSO017G5375' => 'pso', 'PSO206G0041' => 'pso', 'PSO210G0166' => 'pso', 'PSO339G6450' => 'pso', 'PSO478G2551' => 'pso', 'PSO832G2742' => 'pso', 'QL03p056871' => 'qlo', 'QL06p004131' => 'qlo', 'QL08p058018' => 'qlo', 'RcHm_v2.0_Chr1g0365691' => 'rch', 'RcHm_v2.0_Chr4g0396121' => 'rch', 'RcHm_v2.0_Chr4g0418191' => 'rch', 'RcHm_v2.0_Chr4g0418241' => 'rch', 'RcHm_v2.0_Chr4g0418281' => 'rch', 'RcHm_v2.0_Chr4g0432741' => 'rch', 'RcHm_v2.0_Chr7g0218781' => 'rch', 'Rhsim02G0019900' => 'rsi', 'Rhsim12G0039300' => 'rsi', 'Rhsim12G0108300' => 'rsi', 'RhsimUnG0097100' => 'rsi', 'Sabra08G0036000' => 'sbr', 'Sabra10G0010600' => 'sbr', 'Sabra10G0163000' => 'sbr', 'SalBow2G1810' => 'sbo', 'SalBow2G1851' => 'sbo', 'SalBow8G4027' => 'sbo', 'Sc09g0007290' => 'sci', 'Sc11g0000880' => 'sci', 'Sc13g0004020' => 'sci', 'Sed0003077' => 'sed', 'Sed0003157' => 'sed', 'Sed0003274' => 'sed', 'Sed0008542' => 'sed', 'Sed0009905' => 'sed', 'Sed0011500' => 'sed', 'Sed0015325' => 'sed', 'Sed0025182' => 'sed', 'SEGI_21106' => 'sgi', 'SEGI_25836' => 'sgi', 'SEGI_28080' => 'sgi', 'SEGI_36739' => 'sgi', 'SGA_v2.0_scaffold39G15345' => 'sas', 'SGA_v2.0_scaffold87G27059' => 'sas', 'SHI08979' => 'shi', 'SHI10223' => 'shi', 'SHI38902' => 'shi', 'SMO014G0014' => 'smo', 'SMO117G0195' => 'smo', 'SMO145G0230' => 'smo', 'SMO203G0164' => 'smo', 'SMO356G0530' => 'smo', 'Solyc01g080040.3' => 'sly', 'Solyc05g013750.3' => 'sly', 'Solyc05g054700.3' => 'sly', 'Sopen01g031820' => 'spe', 'Sopen05g008670' => 'spe', 'Sopen05g033160' => 'spe', 'Sp3g05060' => 'spa', 'Sp3g21290' => 'spa', 'Sp5g07190' => 'spa', 'TAR362G0179' => 'tar', 'TAR374G0790' => 'tar', 'TAR374G1401' => 'tar', 'TAR622G0408' => 'tar', 'TAR633G2416' => 'tar', 'THA.LOC104806415' => 'tha', 'THA.LOC104808667' => 'tha', 'THA.LOC104818795' => 'tha', 'THA.LOC104824258' => 'tha', 'Thecc.02G263500' => 'tca', 'Thecc.04G222600' => 'tca', 'Thecc.04G222800' => 'tca', 'Thecc.10G057500' => 'tca', 'Thhalv10010135m.g' => 'esa', 'Thhalv10021603m.g' => 'esa', 'Thhalv10021629m.g' => 'esa', 'TPR.G15503' => 'tpr', 'TPR.G20112' => 'tpr', 'TPR.G30535' => 'tpr', 'TPR.G6284' => 'tpr', 'TWI09G1392' => 'twi', 'TWI15G1197' => 'twi', 'TWI18G1281' => 'twi', 'TWI36G0021' => 'twi', 'TWI73G0745' => 'twi', 'TWI75G0383' => 'twi', 'unitig_0.g1808' => 'ugi', 'unitig_21.g20402' => 'ugi', 'unitig_22.g6427' => 'ugi', 'unitig_32.g10802' => 'ugi', 'unitig_744.g24416' => 'ugi', 'unitig_748.g8559' => 'ugi', 'vmacro01116' => 'vma', 'vmacro07144' => 'vma', 'vmacro15304' => 'vma', 'VMungo0251G0156' => 'vmu', 'VMungo0331G1034' => 'vmu', 'VMungo1309G1208' => 'vmu', 'VMungo1383G1542' => 'vmu', 'Zm00001eb266320' => 'zma', 'Zm00001eb355580' => 'zma' ) $gf_id = 'HOM05D001370' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001370' ) $data_identifier = 'HOM05D001370' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 2, 'aag' => (int) 3, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 7, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 32, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 6, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 13, 'fve' => (int) 5, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 8, 'cav' => (int) 4, 'hma' => (int) 5, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 9, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 11, 'osa' => (int) 2, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 3, 'ppa' => (int) 4, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 7, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 8, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 3, 'smo' => (int) 5, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb355580' $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